Pick a subsystem you're interested in and dive in. You may want to try to get a broad-strokes overview of the high-level setup, which is presumably why you would start with main, but since other folks have already done the work of that and written about it, I'd say the best approach is to just read their analysis for that info, and dig into specific sub-systems for details that you're interested in.

I'd also caution against putting the Doom 3 code on any sort of pedestal. Its a great resource to have the source of a commercial game as renowned as Doom 3, but there's a lot of other great open-source code too. There was a recent opinion article on the "beauty" of the Doom 3 source code, but exercise caution and judgment, as it was just that--an opinion of one person, who, in the very same article, says that he considers himself "not a coder", although he has published a game himself. Having read that article myself yesterday, much of what he considers "beautiful" are things that myself and others would consider ugly. If you're looking to the code as a model for you to mimic, you could do worse, but you could also do better. Don't assume the code or design is great just because it's Doom, or just because its Carmack.